Palette support in volumes and scale bars

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-02-26)
Description
Hi,

As discussed on the chimera-users message board, I would like to see support for color palettes (setting equally spaced color,threshold pairs from a color palette) and generation of scale bars when coloring planes and solid representation maps.

Cheers
Oli

Log:
> camera ortho

> lighting soft

> set bgColor white

> lighting depthCueColor white

> cofr centerOfView

> volume projectionMode 3d

No volumes specified  

No volumes specified  

UCSF ChimeraX version: 0.9 (2019-02-26)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc

Opened
refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc,
grid size 400,400,400, pixel 1.25, shown at level 0.0284, step 2, values
float32  

> help scolor

No help found for 'scolor'  

> color sample #1 map #1

Map values for surface "level 0.0284": minimum 0.0284, mean 0.04012, maximum
0.1562  

Expected a keyword  

> clip

> color sample #1 map #1

Map values for surface "level 0.0284": minimum 0.0284, mean 0.0284, maximum
0.02841  
Map values for surface "cap front": minimum 0.0114, mean 0.02923, maximum
0.05255  
Fetching compressed palette tainbow from
http://www.colourlovers.com/api/palettes?keywords=tainbow&format=json&numResults=100  

> color sample #1 map #1 palette rainbow

Map values for surface "level 0.0284": minimum 0.0284, mean 0.0284, maximum
0.02841  
Map values for surface "cap front": minimum 0.0114, mean 0.02923, maximum
0.05255  

> color sample #1 map #1

Map values for surface "level 0.0284": minimum 0.0284, mean 0.0284, maximum
0.02841  
Map values for surface "cap front": minimum 0.0114, mean 0.02923, maximum
0.05255  

> ~clip

> clip

> select up

Nothing selected  

> select up

Nothing selected  

> color sample #1 map #1

Map values for surface "level -10": minimum -0.01868, mean -8.096e-05, maximum
0.01763  
Map values for surface "cap front": minimum -0.009887, mean -0.0001083,
maximum 0.01377  

> ~clip

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> volume maximumIntensityProjection true

> volume btCorrection true

> volume btCorrection true

> volume projectionMode 3d

Unknown command: focus  

> view cofr false

Unknown command: cmode rgba  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

Invalid "colorMode" argument: 'rgba' is ambiguous, could be rgba12, rgba16,
rgba4, rgba8  

Invalid "colorMode" argument: Should be one of 'auto12', 'auto16', 'auto4',
'auto8', 'l12', 'l16', 'l4', 'l8', 'la12', 'la16', 'la4', 'la8', 'opaque12',
'opaque16', 'opaque4', 'opaque8', 'rgb12', 'rgb16', 'rgb4', 'rgb8', 'rgba12',
'rgba16', 'rgba4', or 'rgba8'  

> volume colorMode rgba16

Invalid "color" argument: Invalid color name or specifier  

Expected a density maps specifier or a keyword  

> volume #1 level 0,0 color white level 0.01,1 color blue level 0.02,1 color
green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow level 0.03,1 color green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow level 0.03,1 color green level 0.04,1 color
green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow level 0.03,1 color green level 0.04,1 color
blue

> volume #1 level 0,0 color white level 0.02,1 color red level 0.04,1 color
orange level 0.06,1 color yellow level 0.08,1 color green level 0.1,1 color
blue

> volume #1 level 0,1 color white level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color white level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level -10,1 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level -10,0 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

Expected a keyword  

Expected a keyword  

> volume #1 level 0,0 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

Unknown command: background solid black  

> set bgColor black

> volume #1 level 0,0 color black level 0.02,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.07,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.2,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.4,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.2,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> view cofr false

> volume #1 level 0,1 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.04,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.04,1 color red level 0.08,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.04,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.02,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0.01,1 color black level 0.02,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.02,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0 color yellow level 0.11,0 color green level 0.14,0 color
blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0 color yellow level 0.11,0 color green level 0.14,0.1 color
blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0 color yellow level 0.11,0.1 color green level 0.14,0.1
color blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0.1 color yellow level 0.11,0.1 color green level 0.14,0.1
color blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0.1 color
orange level 0.09,0.1 color yellow level 0.11,0.1 color green level 0.14,0.1
color blue

> volume #1 level 0,0 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,0.1 color green level
0.14,0.1 color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,0.1 color green level
0.14,0.1 color blue

> view cofr false

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,0.1 color green level
0.14,1 color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,1 color green level 0.14,1
color blue

Invalid "level" argument: Expected a number  

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,0.1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> clip

> select up

Nothing selected  

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color transparent level 0.05,1 color red level 0.07,1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,1 color transparent level 0.05,1 color red level 0.07,1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> set bgColor white

> volume #1 level 0,0 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0.05,1 color red level 0.07,1 color orange level 0.09,1
color yellow level 0.11,1 color green level 0.14,1 color blue




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.